Variant report

Variant	rs3729841
Chromosome Location	chr19:55665410-55665411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr19:55665112-55665490	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:55658330..55661734-chr19:55662329..55665982,4	MCF-7	breast:
2	chr19:55590321..55593325-chr19:55662374..55666146,3	K562	blood:

Variant related genes	Relation type
TNNT1	TF binding region
ENSG00000267577	TF binding region
ENSG00000131037	Chromatin interaction
ENSG00000105048	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10424609	0.91[ASN][1000 genomes]
rs10424638	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11669300	0.88[ASN][1000 genomes]
rs11670538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672000	0.88[ASN][1000 genomes]
rs11672834	0.88[ASN][1000 genomes]
rs13343638	0.85[ASN][1000 genomes]
rs16986289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs16986292	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16986294	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2365725	0.88[GIH][hapmap]
rs3729837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848617	0.88[GIH][hapmap]
rs3859540	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[ASN][1000 genomes]
rs3859542	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6509927	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6509930	1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[ASN][1000 genomes]
rs7248799	1.00[ASN][1000 genomes]
rs8107129	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107736	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110415	0.91[ASN][1000 genomes]
rs9749340	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3729841	TNNT1	cis	multi-tissue	Pritchard
rs3729841	ZNF787	cis	lymphoblastoid	seeQTL
rs3729841	LOC352909	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55661800-55667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr19:55662000-55667200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr19:55662000-55667400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr19:55662000-55667400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:55662000-55667400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:55663400-55667400	Weak transcription	A549	lung
7	chr19:55663600-55667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:55663600-55667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:55663600-55667400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:55663600-55667400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:55663800-55665600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:55663800-55667200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:55664200-55665600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr19:55664200-55666000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr19:55664400-55666400	Transcr. at gene 5' and 3'	Left Ventricle	heart
16	chr19:55664400-55667400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:55664800-55665600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr19:55664800-55665600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:55664800-55665800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:55664800-55666400	Active TSS	Right Atrium	heart
21	chr19:55665000-55665600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr19:55665000-55666200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:55665200-55665600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:55665200-55665600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:55665200-55665800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:55665200-55666000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr19:55665200-55666000	Transcr. at gene 5' and 3'	Fetal Heart	heart
28	chr19:55665200-55666200	Genic enhancers	K562	blood
29	chr19:55665400-55666400	Transcr. at gene 5' and 3'	Right Ventricle	heart
30	chr19:55665400-55667200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:55665400-55667400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:55665400-55667400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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